Can a virus that has been healed to prevent it becoming a further menace, but not removed, still have enough similarity to its old makeup when it acted as a predator, so as to be seen by the immune system and cause symptoms to reappear? If so, how can the healing be considered effective, as the damaging effects of the immune system in response to viral presence is why such low-level chronic viruses pose a problem to begin with?

For the most part this is not a problem. After all, healing is truly healing, meaning that all major negative influences giving rise to symptoms will have been prevented. Accordingly, the healing of a chronic viral malady necessitates that the virus either be removed or altered in a way to no longer be symptomatic, and that would include changes in its makeup. So the immune system will no longer be triggered, as that is by far the most important cause of the injury to the body, a bystander effect from damage by the immune system attempting to eradicate the virus, seeing it as an intruder, and then launching a kind of chemical warfare.